[gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent

[Mark Abraham]

On 9/03/2012 7:19 AM, bo.shuang wrote:
> Hi,
>
> Thank you for your answer. May I ask where I can find the right 
> parameter in gbsa.itp for ions? These should be very basic things in 
> simulation, but I cannot find their parameters anywhere. How do you 
> guys use implicit solvent if you want to have ions inside?

"Ions inside" is a bit vague for a description, but this kind of thing 
is often a problem. Seee 
http://www.gromacs.org/Documentation/How-tos/Parameterization

Mark

>
> Thank you!
>
> Bo
>
> bo.shuang wrote:
> > For example, if I want to simulate how Membrane phospholipid bilayer
> > form its configuration in water, and want to use CG model and implicit
> > solvent, then I need the heads of these phospholipid molecules to be
> > hydrophilic and their tail to be hydrophobic. How can I specify
> > parameter of these particles to make them have these different
> > properties in implicit solvent?
> > It just an example. Hydrophobic also play important role in protein and
> > DNA folding. That's why I want to make hydrophobic work in implicit
> > solvent. Thank you very much for your help!
> >
>
> Hydrophobicity and hydrophilicity are functions of the nonbonded 
> parameters
> (charges and van der Waals parameters) of the individual atom types, 
> which are
> essential components of a force field.  There's nothing extra you need 
> to do
> beyond defining these parameters (or using those that already exist).
>
> -Justin
>
>

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